Development of T cell receptor repertoires during childhood in health and disease
By Emma A., Bunia A., Othilia FS., Tobias C. & Joanna R.
Group 21
Introduction
Based on the article Mitchell et al. (2022) Allele repertoire development during childhood and type 1 diabetes Two groups of patients, case and control Returns four times for observations
Materials:
1. Data from immunoSEQ ANALYZER
Methods:
1. Base R 1. Tidyverse R 2. PCA analysis 3. MCA analysis
Data Description
Original data (01_dat_load.tsv)
[1] 359 12
# A tibble: 359 × 2 sample_name sample_tags <chr> <chr> 1 310183_TCRB 06 Years, 6 Years at visit, Caucasian, Control, Control 022, GAD… 2 310110_TCRB 0 Years at visit, 09 Months, 6.37808219178082 Years at diagnosis… 3 310206_TCRB 0 Years at visit, 10 Months, 10.558904109589 Years at diagnosis,… 4 310288_TCRB 09 Years, 9 Years at visit, 9.56986301369863 Years at diagnosis,… 5 310271_TCRB 02 Years, 2 Years at visit, 6.87397260273973 Years at diagnosis,… 6 310244_TCRB 05 Years, 18.0438356164384 Years at diagnosis, 5 Years at visit,… 7 310137_TCRB 07 Years, 7 Years at visit, Caucasian, Control, Control 014, Fem… 8 310258_TCRB 12 Years, 12 Years at visit, 12.958904109589 Years at diagnosis,… 9 310127_TCRB 04 Years, 11.6821917808219 Years at diagnosis, 4 Years at visit,…10 310300_TCRB 17 Years, 17 Years at visit, 17.7561643835616 Years at diagnosis…# ℹ 349 more rows
Discuss the implications of your findings. Interpret the results and relate them to your objectives.
Implications of findings
Patterns exist between the different mean antibody expressions. Suggests need for PCA. .
Two components explain majority of variance in data. Components are used to express the rotation matrix.
The rotation matrix shows the variance between the variables. Two clusters form between the four variables, each more strong associated with each of the two component.
The HLA analysis suggests alleles of interest, by indicating dominant subtypes in case subjects, compared to control.
MCA…
Limitations
Missing values for control subjects
Conclusion
Clear differences exist between case and control subjects, both in terms of antibody expression and in terms of allele subtypes.
Suggests that both antibody expression and allele subtype are involved in the development of diabetes in children.
Based on our results, HLA-DQB1*0202, HLA-B*4402, HLA-A*2402, and HLA-B*0702 could have a direct influence on type 1 diabetes.